A list of common infected applications and clean alternatives:
I've just started this list to answer all those questions about alternatives to spyware-infected applications. I will update this list from time to time as I come across other examples.
File sharing (aka P2P) applications that are infected with spyware or similar kinds of malware:
Grokster
Kazaa
File sharing applications that are clean (read also a SpywareInfo article about them):
BitTorrent
Direct Connect (displays ads though)
Shareaza
Download managers that are infected with spyware or adware (read also our download managers article):
Download Accelerator Plus (contains ads and possible spying, tested version: 7)
FlashGet (Cydoor, tested version: 1.40, paying customers can install it ad-free)
Gozilla (eZula and Radiate, tested version 1.44.39)
NetAnts (Cydoor, tested version: 1.25)
Download managers that are clean:
Download Express (tested version: 1.5 Build 233 SR 1)
FreshDownload (tested version: 6.50)
GetIt (tested version: 1.04)
GetRight (tested version: 5.02)
LeechGet 2003 (recommended, tested version: 1.0 Build 1500 RC3)
Net Transport
ReGet (tested version: Deluxe 3.3)
Star Downloader (tested version: 1.42)
WGET (recommended, a command line utility, tested versions: 1.6.x to 1.8.1)
Password managers that are infected with spyware or similar kinds of malware:
Gator eWallet is coming from the company Claria, formerly known as GAIN, formerly known as Gator. eWallet is advertised as the world's most popular digital wallet, which may be due to the fact that many users don't know that they get it, as different Gator apps are often bundled with software like P2P installers. The eWallet itself is not bad, but I would simply not trust an advertisement company to handle all my passwords when there are better alternatives.
Password managers that are clean:
RoboForm is a nice and clean password manager, supporting IE as well as Mozilla (sadly, no Opera yet). And a very nice thing is that you can sync your passwords with a special Palm or Pocket PC application, carrying your passwords always with you - in a well-encrypted form of course.
The Mozilla and Firefox browsers have an integrated password manager, but it's data is not well-protected.
Internet Explorer has a password management as well, but complete solutions like RoboForm will give you a lot more features.